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I sincerely believe that empathy is a very strong emotion that doesn't need much training
but to believe that even killing our food creates a feeling of empathy?
No!
That part is purely conditioned in a society where we never have to kill for food, actually, where killing is negatively treated in any case
(a society that you have been subjected to before starting utilitarian killing as well)

here I point to the empathy for food/empathy for that which you made an attachment with
Best working example I can think of is my grandfather (an oldfashioned farmer),
who had no emotional attachments to the animals he slaughtered (boiling chicks alive to feed to the pig),
but couldn't take his dogs to the vet to be put down and had to have someone else do it

No argument there

So, are we talking from an instinctive or indoctrinated PoV?
Where do emotions stop and taught behavior begin?

We instinctively form attachments (even to inanimate objects), but when it comes to empathy vs morals,
I believe empathy is where we care about those in our direct enviroment and social morals
when it concerns the impersonal people/(animals) of the world

Just look at how empathy went out of the window when the media showed looters in New Orlean
in the aftermath of Katrina were running off with luxury items
(which were the exceptions since most looters went for basic necessities)

Actually, I'm a vegetarian, so I don't eat animals.

My experiences killing animals have all been mercy killings, a surprisingly common occurrence in my life. I've often had cats who bring me badly wounded animals and often times when killing mice with snap traps, I'll encounter one whose back legs have been broken by the trap but who is still alive. In both cases I will break their necks, since they would otherwise be forced to endure a much slower death.

But it still makes me feel sad even though I know it is the humane thing to do.

As for the different layers of empathy, I agree that we have greater empathy for those who are close to us. But there is also a kind of empathy that most empathic people feel for even complete strangers.

I mean if you encounter a badly injured person in a car accident, anyone would stop and call for help, unless it was obvious that someone had done so already.

It's true that there is a logical reason to help that person, but it's not logic that causes us to act this way, it is usually empathy.